I think she should come from a different dimension that can be accessed through a portal on Earth. Do the same for Aquaman and Darkseid. They could make it so that the world engine opened up these portals during Man of Steel.

EDIT: The Themyscira portal would be up in the sky, the Atlantis portal would be deep underwater, and the Apokolips portal would be in a volcano.

Darkseid having a portal works, but I don't think Aquaman should have one. I think he should be at the depths of an ocean (a lost city undiscovered by humans because of the sheer depth).